Closed jantrienes closed 2 years ago
I found it relatively hard to install the dependencies on a non-linux system. This PR adds a dockerized runtime which hopefully makes it easier to get started with chexpert-labeler.
Testing done:
$ docker build -t chexpert-labeler:latest . [+] Building 24.4s (17/17) FINISHED => [internal] load build definition from Dockerfile 0.0s => => transferring dockerfile: 804B 0.0s => [internal] load .dockerignore 0.0s => => transferring context: 142B 0.0s => [internal] load metadata for docker.io/continuumio/miniconda:latest 0.0s => [ 1/12] FROM docker.io/continuumio/miniconda 0.0s => [internal] load build context 0.0s => => transferring context: 42.84kB 0.0s => CACHED [ 2/12] RUN apt-get update --allow-releaseinfo-change 0.0s => CACHED [ 3/12] RUN mkdir -p /usr/share/man/man1 0.0s => CACHED [ 4/12] RUN apt-get install -y default-jre 0.0s => CACHED [ 5/12] WORKDIR /app/chexpert-labeler 0.0s => CACHED [ 6/12] RUN git clone https://github.com/ncbi-nlp/NegBio.git 0.0s => CACHED [ 7/12] COPY environment.yml environment.yml 0.0s => CACHED [ 8/12] RUN conda env create -f environment.yml 0.0s => [ 9/12] COPY . . 0.0s => [10/12] RUN chmod +x ./entrypoint.sh 0.2s => [11/12] RUN ./entrypoint.sh python -m nltk.downloader universal_tagset punkt wordnet 7.6s => [12/12] RUN ./entrypoint.sh python -c "from bllipparser import RerankingParser; RerankingParser.fetch_and_load('GENIA+PubMed')" 15.6s => exporting to image 0.8s => => exporting layers 0.7s => => writing image sha256:0e836ce35a8afff3924177b9f182635c01a1b142bcd383e2d4df4a529451363d 0.0s => => naming to docker.io/library/chexpert-labeler:latest $ docker run -v $(pwd):/data chexpert-labeler:latest python label.py --reports_path /data/sample_reports.csv --output_path /data/labeled_reports_docker.csv Generating LALR tables Downloading 'http://search.maven.org/remotecontent?filepath=edu/stanford/nlp/stanford-corenlp/3.5.2/stanford-corenlp-3.5.2.jar' -> '/root/.local/share/pystanforddeps/stanford-corenlp-3.5.2.jar' $ diff labeled_reports.csv labeled_reports_docker.csv && echo "equal" equal
I found it relatively hard to install the dependencies on a non-linux system. This PR adds a dockerized runtime which hopefully makes it easier to get started with chexpert-labeler.
Testing done: